can't get toilet flush with floor after installing new wax ring

hey guys, fran here.
having issues with reinstalling my toilet. i just installed new slate tile and put a new flange in where the old was.
i ended up getting one of those flanges that fits inside the 3" pipe and not the regular ones that fits outside the pipe. it's a long story as to why, but is that ok to use?
so, after i tiled, i ended up tiling too close to the pipe, so i had to dremel out some thinset and some of the slate so the flange would sit flush on top of the new tile. that was completed and leveled, and screwed through the flooring with stainless steel screws.
so everything looked perfect - dry installed the toilet without the wax ring and it sat flsuh on the floor. so far so good, but when i installed the wax ring onto the flange and then sat the toilet on top, the toilet is now about 1/4" to 1/2" off the floor.
what do i do to get the toilet to be flush? do i push it down onto the wax ring? seems right now it's not going any further down.
do i need to lower the flange? find some shims?
i can post pictures tonight if you'd like to see what it looks like. please tell me i don't need to unscrew the flange just for a picture - i don't want to strip the screws.
help!
thanks guys!
fran

I realize it's already a done deal, but it was not a good idea to use a 3" flange that fit inside the pipe. These cut the inside diameter of the pipe too much and can, operative word, "can", cause problems with clogging. I hope you will not have this problem, but if you do start having clogs, that may well be the cause and have to be dealt with. Those rings with the plastic horns should be outlawed. Problem is, they look like a great idea, but in reality, they cause problems, and not just the one you had.